Of potential interest here: Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic | bioRxiv
(and see this thread on the subject: https://twitter.com/jbloom_lab/status/1407445604029009923).
The interesting new facts: 1) evidence that SARS-CoV-2 was circulating in Wuhan prior to the seafood market outbreak, and 2) that evidence was deleted from public databases, presumably at the request of the researchers.
This does not have a good odor about it.
It appears to me (a non-expert in phylogenetics) that a furin cleavage site independently evolved in several lineages, or there were independent deletions. Does that sound correct?
If so, this would mean a furin cleavage site evolved naturally in several betacoronavirus lineages.
LOL twitter was banned in my country and those who use it will be prosecuted by the government.
Indeed, an example of âthe coverup is worse than the crimeâ. If I am reading the paper correctly, the samples were collected in Feb 2020, so it doesnât contradict the original story of the virus appearing in Dec 2019. The virus was just 3 mutations away from the Wuhan reference, so I canât see how the actual sequences are incriminating in any way. Why would they have this data removed from SRA? Afraid of people accusing them of not detecting it earlier, or containing it?
If I am missing anything, please let me know.
Yeah, these sequences provide some further evidence that the virus was circulating before the known outbreak at the market, but there was already evidence for that. That by itself isnât really indicative of anything â the circulation might not even have been in humans. The data removal could mean that somebody knew there was something that needed to be hidden and was just removing as much data as possible, or that the government was generally being secretive and restricting information as a matter of principle/habit.
This find neither settles any questions nor provides any reassurance. Blech.
Hadnât thought of that angle. Good point. I trust Youtube videos as far as I can throw them, but one video made in interesting claim. He thought the Chinese government is solely focused on the problems right in front of their noses, and that they donât have any type of long term plan. Mass removal of data without understanding the public relations consequences would fit into that pattern of behavior.
My thoughts exactly. I want to give China the benefit of the doubt, but they make it hard to do so.
There was a database that the WIV took down in September because it was being hacked. I donât know if that is what he is talking about. If so, itâs hard to see the line of logic here that would lead to the conclusion that the lab was covering up its involvement in a pandemic that would not occur for another three monthsâŚ
Heâs talking about raw sequence data removed from the Sequence Read Archive, which is an international database of public sequence data.
How would Baltimore know this? We can only wish we had an inventory of all that was out there. That is why we have virology labs, to at least start to get a grip on the phylogeny and etiology of zoonotic disease.
Responses to the Bloom paper. It seems it may be another smoking gun that isnât.
The one thing it isnât is a smoking gun. It is, however, both curious and unfortunate.
glipsnortSteve SchaffnerComputational Biologist
Faizal_Ali
The one thing it isnât is a smoking gun. It is, however, both curious and unfortunate.
From 46:15 â 53:00 mins:
Bloom acknowledges that researchers can piece together the coronavirus sequences from the data found in the Small paper, but he says thatâs not the way most in the field conduct evolutionary analyses of SARS-CoV-2. âNo one knew about these sequences because the way that people find sequences is to go to the sequence databases and download the sequences and look at them,â Bloom says.
So no important information was hidden. It was just not in one particular place. I donât know how unusual it is for researchers to remove data from the website. But if they were trying to cover something up, publishing the data on a journal article seems a strange way to go about it.
Well, thatâs two clips from his livestream Iâve seen, and theyâve both been terrible. The clear message in this clip is that anyone who doesnât trust the Chinese government is motivated by racism, a message that is both objectively stupid and morally reprehensible.
Clearly the researchers who published the paper were not trying to hide anything, and there could be benign reasons for removing the data. The question is whether they did so at the instruction of their government. If, as is reportedly the case, they havenât resubmitted the data elsewhere (as they said they would), that is troubling.
I disagree. SARS2 is the only sarbecovirus (betacoronaviruses belonging to clade B) that has a FCS.
Moreover, it has been found that all Spike with a SARS-CoV-2 Spike sequence homology greater than 40% did not possess a furin cleavage site, including Bat-CoV RaTG13 and SARS-CoV (with sequence identity as 97.4% and 78.6%, respectively). What this means is that the viruses that are phylogenetically closest to SARS2, i.e. those that can recombine with each other, do not have an FCS. This makes the FCS a quite strange feature of SARS2.
âMoreoverâ? The first sentence says the same as the second. Repeating a point in more words does not increase the amount of evidence.
What this means is that the viruses that are phylogenetically closest to SARS2, i.e. those that can recombine with each other, do not have an FCS. This makes the FCS a quite strange feature of SARS2.
And thatâs three viruses. Among the three known viruses in that clade, itâs the only one with a furin cleavage site. Iâd like to see a reference that substantiates the implied claim that sequence similarities below those mentioned prevent reassortment/recombination.
Edit: Found this preprint which appears to detail evidence that betacoronaviruses are performing recombination in(among other ORFs) their spike proteins with highly divergent viruses:
The spike gene is a striking recombination hotspot among SADSr-CoVs. Due to the clustering of putative breakpoints surrounding the 5â end, 3â end, and middle of spike, we ran IDPlot on subsets of three viruses â SADSr-CoV/162140 (reference), SADSr-CoV/141388 or SADS-CoV/FarmA, and a virus of interest from the larger dataset. We found breakpoints delineating six distinct and highly divergent spike genes among the eight analyzed viruses ( Figure 5B ), which reflects recombination events encompassing either the entire spike or the S1 subunit that mediates receptor binding. There are 3 unique full-length spikes (BtCoV/RfY2012, HKU2r-BtCoV/160660, BtCoV/HKU2) with 63-73% nucleotide identity to the reference sequence and two unique S1 domains (SADSr-CoVs/8462 and 8495) with <80% identity to the reference ( Figure 5B, S7A ). Some of these regions match with high identity to partial sequences in GenBank (indicated by an asterisk in Figure 5B) which may be either the source of the recombinant spike or different isolates of the same virus for which a full-length genome is available. Other spikes in this dataset are clearly divergent from any other known sequence.
In addition to spike, accessory proteins that target innate immunity can play important roles in host range and pathogenesis [34]. We found a second recombination hotspot surrounding the accessory gene Orf7a, which rivals spike gene diversification. Specifically, our dataset contained five distinct Orf7a genes, some of which lack any closely related sequences in GenBank ( Figure 5C, S7A ).
The SADSr-CoV lineage is rapidly diversifying via recombination, particularly in the spike and ORF7a accessory genes. We observed that numerous viruses with >95-99% identity in conserved Orf1ab regions contain highly divergent spike and accessory genes which may shift host range and virulence in otherwise nearly isogenic viruses. These findings highlight that viruses sampled to date represent only a sliver of existing coronavirus diversity and that coronaviruses can change rapidly, drastically, and unpredictably via recombination with both known and unknown lineages. The SADSr-CoVs exemplify the potential of coronavirus to rapidly evolve through promiscuous recombination.
The phylogeny of the larger betacoronavirus clade demonstrates that the FCS has naturally evolved independently in many of those branches. Thatâs what you keep ignoring. Evolving an FCS has happened in the wild, so why would an FCS indicate modification in the lab?
Thereâs also some Texas sharpshooter fallacy going on here. There are lots and lots of unlikely things that could turn up in a novel virusâs genome. Even if an FCS were quite unlikely to evolve, finding some unlikely thing isnât unlikely at all.
Update: Also found this article which shows that another close relative RmYN02 (93.3 whole genome similarity) of SARS-Cov2, also has a polybasic furin cleavage(though not identical to SARS-Cov2âs) insertion in itâs spike protein:
https://www.sciencedirect.com/science/article/pii/S096098222030662X
From Figure 2H:
The S protein of CoVs is functionally cleaved into two subunits, S1 and S2 [16], in a similar manner to the haemagglutinin (HA) protein of avian influenza viruses (AIVs). The insertion of polybasic amino acids at the cleavage site in the HAs of some AIV subtypes is associated with enhanced pathogenicity [17, 18]. Notably, SARS-CoV-2 is characterized by a four-amino-acid insertion at the junction of S1 and S2, not observed in other lineage B beta-CoVs [19][20]. This insertion, which represents a poly-basic (furin) cleavage site, is unique to SARS-CoV-2 and is present in all SARS-CoV-2 sequenced so far. The insertion of three residues, PAA, at the junction of S1 and S2 in RmYN02 (Figure 2H; Figure S2A for results from Sanger sequencing) is therefore of major importance. Although the inserted residues (and hence nucleotides) are not the same as those in RmYN02, and hence are indicative of an independent insertion event, that they are presented in wildlife (bats) strongly suggests that they are of natural origin and have likely been acquired by recombination. As such, these data are strongly suggestive of a natural zoonotic origin of SARS-CoV-2.
